Re: [AMBER] Lipid diffusion in cpptraj

From: Daniel Roe <>
Date: Thu, 2 Jul 2015 10:36:20 -0600


You may want to try the 'stfcdiffusion' command instead as this can
explicitly calculate diffusion in the XY plane (see manual for full
syntax). Also make sure you are using the latest version of cpptraj (15).


On Wednesday, July 1, 2015, Life Sciences Inc <> wrote:

> Dear all
> 1) I have two questions regarding lateral diffusion of lipids in a bilayer,
> I want to calculate diffusion in two dimensions X and Y, how to calculate
> it in cpptraj?
> I have total system with atoms 102220, total number of water 15640 and 400
> lipid molecules, 16140 residues, time per frame in my trajectory is 5 ps. I
> want to calculate diffusion for all my lipid molecules in the system.
> After loading the topolgy file and unwraped trajectory in cpptraj I am
> giving the following command to calculate diffusion for my lipid molecule .
> diffusion 5.0 diff.out :1
> I get the following output which is normal;
> Atom Mask is [:1]
> The average and individual results will be printed to:
> diff.out_x.xmgr: Mean square displacement(s) in the X direction (in Å^2).
> diff.out_y.xmgr: Mean square displacement(s) in the Y direction (in Å^2).
> diff.out_z.xmgr: Mean square displacement(s) in the Z direction (in Å^2).
> diff.out_r.xmgr: Overall mean square displacement(s) (in Å^2).
> diff.out_a.xmgr: Total distance travelled (in Å).
> The time between frames in ps is 5.000.
> To calculate diffusion constants from a mean squared displacement plot
> (i.e. {_x|_y|_z|_r}.xmgr), calculate the slope of the line and multiply
> by 10.0/6.0; this will give units of 1x10^-5 cm^2/s
> but;
> whenever I open xmgr files they are empty and of 0 bytes size. I cannot
> understand what is happening, can anyone let me know where I am making the
> mistake.
> 2) I want to calculate lipid jumps throughout the system as well if anyone
> have scripts or did such analysis kindly guide me;
> My idea is to calculate centre of mass for the system and then from that
> centre of mass around it jumps/lateral dffusion in specific direction can
> be calculated say 5 angstrom around COM and in this way for the whole
> system. I think stfcdiffusion is somewhat close to my idea but I dont know
> how to calculate the COM and what should be the total distance in which I
> have to calculate the diffusion (by dividing in to shorter distances and
> for each distance diffusion from COM must be calculated, int his way for
> the whole system ).
> I would be really grateful for any help
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jul 02 2015 - 10:00:02 PDT
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